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- PDB-3p0z: Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate... -

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Basic information

Entry
Database: PDB / ID: 3p0z
TitleCrystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Burkholderia pseudomallei with cytidine and FOL955, 4-(1H-imidazol)-1-yl)phenol
Components2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
KeywordsLYASE / Seattle Structural Genomics Center for Infectious Disease / SSGCID / IspF / cytidine / FOL955 / MEP pathway / isoprene biosynthesis / MSR / metal-binding
Function / homology
Function and homology information


2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / metal ion binding
Similarity search - Function
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, conserved site / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase superfamily / YgbB family / 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase signature. / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE / : / 4-(1H-IMIDAZOL-1-YL)PHENOL / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Citation
Journal: J Struct Funct Genomics / Year: 2011
Title: Leveraging structure determination with fragment screening for infectious disease drug targets: MECP synthase from Burkholderia pseudomallei.
Authors: Begley, D.W. / Hartley, R.C. / Davies, D.R. / Edwards, T.E. / Leonard, J.T. / Abendroth, J. / Burris, C.A. / Bhandari, J. / Myler, P.J. / Staker, B.L. / Stewart, L.J.
#1: Journal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.
History
DepositionSep 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2013Group: Database references
Revision 1.3Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
B: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
C: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,62212
Polymers58,4613
Non-polymers1,1619
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8780 Å2
ΔGint-144 kcal/mol
Surface area15680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.550, 67.630, 59.770
Angle α, β, γ (deg.)90.00, 95.99, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase / / MECPS / MECDP-synthase


Mass: 19487.109 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: ispF, BURPS1710b_2511 / Production host: Escherichia coli (E. coli)
References: UniProt: Q3JRA0, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

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Non-polymers , 6 types, 282 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MSR / 4-(1H-IMIDAZOL-1-YL)PHENOL


Mass: 160.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8N2O
#5: Chemical ChemComp-CTN / 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE / CYTIDINE / Cytidine


Mass: 243.217 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H13N3O5
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.13 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 27 mg/mL protein in 20% PEG 4000, 100 mM Tris, 200 mM NaCl, 5 mM ZnCl2. Crystals soaked in 25 mM cytidine and FOLMSR in same buffer for 3 weeks., pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 31, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. obs: 33803 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.056 / Net I/σ(I): 17.91
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.95-20.4262.1197.5
2-2.060.3322.6199.4
2.06-2.120.2343.9198.8
2.12-2.180.2045.11100
2.18-2.250.2325.9199.5
2.25-2.330.2627.3196.9
2.33-2.420.178.5199.7
2.42-2.520.1859.8198.7
2.52-2.630.13412.2199
2.63-2.760.09714.1199.5
2.76-2.910.09417.3199.5
2.91-3.080.0622.71100
3.08-3.30.0725.5199.2
3.3-3.560.04135.41100
3.56-3.90.0343.9199.7
3.9-4.360.02650.5199.9
4.36-5.030.02257.2199.6
5.03-6.170.02353.6199.8
6.17-8.720.02256.7199.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→19.83 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 6.275 / SU ML: 0.085 / SU R Cruickshank DPI: 0.1454 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19102 1712 5.1 %RANDOM
Rwork0.15226 ---
obs0.15425 32038 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.989 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.95→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3402 0 68 273 3743
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0213566
X-RAY DIFFRACTIONr_bond_other_d0.0010.022359
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.9954848
X-RAY DIFFRACTIONr_angle_other_deg0.94935720
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6925465
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.39723.072153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.95415538
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4411535
X-RAY DIFFRACTIONr_chiral_restr0.0920.2564
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214069
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02747
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7311.52294
X-RAY DIFFRACTIONr_mcbond_other0.2281.5956
X-RAY DIFFRACTIONr_mcangle_it1.20923622
X-RAY DIFFRACTIONr_scbond_it2.11631272
X-RAY DIFFRACTIONr_scangle_it3.0574.51224
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 118 -
Rwork0.237 2328 -
obs--97.64 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.01630.47810.43971.79710.63582.236-0.0440.09310.1618-0.18070.0420.0264-0.12460.1080.0020.07540.0095-0.01980.0390.01880.082412.2132-34.8845-13.505
23.28740.28690.01933.4189-0.49440.7614-0.0207-0.24450.59880.2069-0.10340.1398-0.3429-0.07750.12410.19670.012-0.01260.0988-0.06920.20728.2779-25.2723-1.9267
31.6071-0.18860.95850.01450.82373.408-0.06130.14420.03660.0244-0.02050.0798-0.025-0.08130.08180.0931-0.00580.00870.0610.01780.09135.9556-35.8663-17.7926
43.61613.02537.9866-5.62696.289919.89510.04080.82270.53140.1291-0.2679-0.1514-0.6236-1.53280.2270.44420.1686-0.05890.62870.09780.5236-3.3162-24.8798-16.905
51.84150.23020.42920.8513-0.29151.39920.0421-0.0206-0.02620.00110.03360.03090.0823-0.0993-0.07580.06940.00080.01950.02070.01180.03285.7105-39.6873-9.8431
61.9391-0.2802-1.28023.6227-0.78291.73240.0467-0.1965-0.11640.23410.0484-0.09920.14540.1092-0.09510.10050.01220.00160.07410.01060.06467.5112-40.679-0.0906
72.55482.0297-0.13153.5653-0.40991.25680.0296-0.16610.01650.1612-0.085-0.0938-0.010.13860.05530.09730.0082-0.00840.0417-0.0030.064518.4054-36.1794-4.5712
82.62912.69481.44997.01432.72372.371-0.07690.07640.0193-0.07390.06280.0010.03780.07310.0140.07440.00680.00470.02620.01690.04413.2873-39.3087-13.3653
93.45922.01153.91055.3312.700511.05370.43010.8499-0.64470.4669-0.0750.09730.7557-0.0973-0.35510.20270.0717-0.02160.1655-0.17570.285620.4691-57.4014-19.0988
102.20570.36561.17483.3232-0.15992.0239-0.26360.72420.4297-0.19680.1454-0.1305-0.31420.49680.11820.0945-0.10480.03220.35380.14840.146224.2532-28.8782-30.3723
119.696110.74049.240914.8024-7.83769.0561-0.35860.97820.60670.1301-0.1014-0.1157-0.19830.84580.460.1841-0.16430.03780.57940.26880.230326.7947-24.7277-32.2281
123.069-0.18620.87621.6904-1.13830.2643-0.02980.6934-0.0297-0.35920.0291-0.2470.22940.34130.00070.13550.04740.05720.3842-0.06420.104327.4807-43.1126-26.6354
1318.169-2.83161.56712.22890.34983.4349-0.42271.22280.7682-0.06430.2016-0.5297-0.6231-0.18760.22110.3170.01870.11990.5557-0.06320.30831.3735-42.7288-33.2807
145.8051.9276-0.12780.4009-2.05566.09710.06671.0121-0.4264-0.1716-0.2271-0.41350.17180.85510.16030.23030.11260.08120.5261-0.17890.206926.2202-51.2548-32.5255
151.90860.30391.20871.50850.48351.5534-0.07820.4250.1884-0.0958-0.00150.073-0.09860.33170.07970.0608-0.02270.01560.14850.04770.044616.1216-34.6539-26.0242
160.50541.27751.60247.0679-2.88634.33230.27890.5816-0.3671-0.08330.0013-0.09280.7230.4018-0.28020.18310.1565-0.07110.1738-0.14970.149619.2289-55.982-24.0201
175.03782.8530.1654.2507-0.20590.74910.07420.117-0.08540.15810.0147-0.13830.08710.1774-0.08890.11270.0462-0.00250.0575-0.01540.060925.4468-42.2599-7.9763
182.9012-0.5025-0.0989.71692.24833.37620.0268-0.19390.24540.4173-0.1053-0.8312-0.1540.43490.07840.09090.0158-0.07610.17910.01260.236642.048-37.6794-5.9122
191.8063-0.54921.11550.7183-0.23540.8170.0506-0.0576-0.16320.20620.046-0.12590.06280.009-0.09660.15460.0453-0.02580.08150.01050.120125.2225-45.7813-4.0234
2029.01510.3819-7.18672.1375-0.34576.0908-0.1884-2.77720.75110.64920.2918-0.3385-0.06770.422-0.10340.37890.078-0.10720.3349-0.07540.208629.3278-45.55495.3747
211.3618-0.16270.31911.2294-0.80441.72130.05560.0196-0.28240.07930.0179-0.1130.19010.1792-0.07350.10890.0726-0.02560.0592-0.00440.114628.0015-50.7849-5.6131
222.3668-0.01750.7054.9838-1.02332.01970.16370.453-0.174-0.2771-0.2507-0.37940.2570.46310.08710.10120.11430.02760.18950.00850.161138.8319-47.757-13.4508
232.5250.05410.56452.99880.02971.4531-0.08160.40180.0169-0.04330.0702-0.23950.06650.45820.01140.0510.02460.00680.16050.00820.058531.7412-39.8044-15.1383
2426.702513.4244-8.614715.6621-2.76968.44230.5149-0.5954-1.35351.1269-0.4358-0.41960.6058-0.1663-0.07910.30790.0206-0.04750.04630.04310.218316.7273-58.4664-7.9119
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 18
2X-RAY DIFFRACTION2A19 - 38
3X-RAY DIFFRACTION3A39 - 64
4X-RAY DIFFRACTION4A65 - 72
5X-RAY DIFFRACTION5A73 - 108
6X-RAY DIFFRACTION6A109 - 122
7X-RAY DIFFRACTION7A123 - 145
8X-RAY DIFFRACTION8A146 - 158
9X-RAY DIFFRACTION9B1 - 5
10X-RAY DIFFRACTION10B6 - 29
11X-RAY DIFFRACTION11B30 - 38
12X-RAY DIFFRACTION12B39 - 60
13X-RAY DIFFRACTION13B61 - 76
14X-RAY DIFFRACTION14B77 - 93
15X-RAY DIFFRACTION15B94 - 153
16X-RAY DIFFRACTION16B154 - 159
17X-RAY DIFFRACTION17C1 - 17
18X-RAY DIFFRACTION18C18 - 39
19X-RAY DIFFRACTION19C40 - 58
20X-RAY DIFFRACTION20C59 - 74
21X-RAY DIFFRACTION21C75 - 103
22X-RAY DIFFRACTION22C104 - 122
23X-RAY DIFFRACTION23C123 - 154
24X-RAY DIFFRACTION24C155 - 159

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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